William Crean allegedly set the fire at 21 Latin Lounge at 122 Westchester Square around 6 a.m. on March 22, fire officials said.
The fire quickly expanded to five adjoining businesses: National Restaurant, Rose Nail Salon, Peking House, Osvaldo Barber Shop and On the Square Flower Shop.
"Obviously, we're relieved that there is some closure to this, albeit such a tragic ending to this story," said John Bonizio, President of the Association of the Merchants & Business Professionals of Westchester Square. "We're grateful that the New York City Fire Department was able to do such a thorough job in this investigation."
The damage from the fire resulted in $2 million in property damage, the structural collapse of 21 Latin Lounge and partial collapses of several of the other stores.
All the affected businesses except National Restaurant have since reopened in Westchester Square, although some in different storefronts.
The Fire Department was mum on Crean's motives for setting the fire, saying only that the investigation was ongoing.
"They're still trying to figure it out and sort it out," said an FDNY spokesperson. "Why he was doing this we don't know, but he did."
Fire marshals identified Crean through surveillance video, said an FDNY spokesperson.
The three-alarm blaze required 33 units, 140 firefighters and nearly three hours to bring under control.
Three firefighters were taken to Jacobi Medical Center for nonlife-threatening injuries.
Crean is charged with second-degree arson and reckless endangerment punishable by up to 25 years in prison.
He will likely face assault charges based on the injuries sustained by the three fire fighters who went to Jacobi, sources said.
Fire marshals from the FDNY Bureau of Fire Investigation and federal agents from the Bureau of Alcohol, Tobacco and Firearms arrested Crean on Monday.
"This investigation demonstrates the outstanding work of the FDNY Bureau of Fire Investigation," said Fire Commissioner Nicholas Scoppetta.
"We are also proud to have an excellent working relationship with the Bureau of Alcohol, Tobacco and Firearms as we work toward a common goal: putting arsonists behind bars."